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Magnesium in PDB 5gwi: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi was solved by Y.R.Wang, S.F.Chen, C.C.Wu, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.788, 176.966, 94.528, 90.00, 112.30, 90.00
R / Rfree (%) 21.4 / 25.3

Other elements in 5gwi:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R also contains other interesting chemical elements:

Platinum (Pt) 4 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R (pdb code 5gwi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gwi

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Magnesium binding site 1 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:49.5
occ:1.00
 OD2 A:ASP559 2.4 33.5 1.0
O A:HOH1412 2.5 42.0 1.0
OD2 A:ASP557 2.6 61.8 1.0
CG A:ASP559 3.5 32.4 1.0
CG A:ASP557 3.6 56.6 1.0
OD1 A:ASP559 3.8 40.1 1.0
CB A:ASP557 3.9 46.2 1.0
OE2 A:GLU477 4.1 53.2 1.0
OP1 C:DC8 4.1 47.6 1.0
O3' C:DC8 4.3 49.1 1.0
C5' C:DC8 4.3 36.6 1.0
CD A:GLU477 4.7 56.5 1.0
CB A:ASP559 4.7 27.8 1.0
OE1 A:GLU477 4.7 58.7 1.0
OD1 A:ASP557 4.8 69.4 1.0
C4' C:DC8 5.0 39.1 1.0
O5' C:DC8 5.0 38.3 1.0

Magnesium binding site 2 out of 6 in 5gwi

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Magnesium binding site 2 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:54.9
occ:1.00
 O A:GLY868 3.2 48.5 1.0
O A:ASN867 3.2 51.6 1.0
OE1 A:GLU870 3.8 76.6 1.0
OP1 C:DG5 3.8 50.8 1.0
C A:GLY868 4.3 42.0 1.0
C A:ASN867 4.4 42.4 1.0
CG A:GLU870 4.6 43.9 1.0
CD A:GLU870 4.6 63.4 1.0
O A:HOH1443 4.7 37.8 1.0
O A:SER794 4.7 35.0 1.0
OD1 A:ASN786 4.8 33.4 1.0
OD1 A:ASN795 4.8 38.0 1.0
CA A:GLY868 4.9 39.9 1.0

Magnesium binding site 3 out of 6 in 5gwi

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Magnesium binding site 3 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:44.4
occ:1.00
 OD2 B:ASP557 2.4 54.6 1.0
O B:HOH1420 2.4 35.8 1.0
OD2 B:ASP559 2.7 35.1 1.0
O E:HOH201 2.9 35.8 1.0
CG B:ASP557 3.4 47.5 1.0
CG B:ASP559 3.7 37.0 1.0
CB B:ASP557 3.8 37.2 1.0
OD1 B:ASP559 4.0 41.9 1.0
OE1 B:GLU477 4.0 36.6 1.0
O3' E:DC8 4.2 49.1 1.0
OP1 E:DC8 4.2 27.5 1.0
C5' E:DC8 4.4 30.1 1.0
OD1 B:ASP557 4.5 76.0 1.0
CD B:GLU477 4.6 47.6 1.0
OE2 B:GLU477 4.6 45.4 1.0
O B:HOH1401 5.0 35.0 1.0
C4' E:DC8 5.0 33.5 1.0

Magnesium binding site 4 out of 6 in 5gwi

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Magnesium binding site 4 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:64.9
occ:1.00
 O D:HOH203 2.5 54.0 1.0
O D:HOH201 2.8 37.9 1.0
O B:HOH1478 3.6 43.3 1.0
O6 D:DG17 4.4 49.6 1.0
O6 D:DG18 4.5 40.6 1.0
O6 E:DG2 4.7 44.8 1.0
N7 D:DG17 4.8 34.5 1.0
N4 E:DC3 4.8 34.0 1.0

Magnesium binding site 5 out of 6 in 5gwi

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Magnesium binding site 5 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:61.8
occ:1.00
 OP1 E:DG5 3.4 46.2 1.0
O B:ASN867 3.9 42.9 1.0
OD1 B:ASN786 4.1 46.3 1.0
O B:SER794 4.2 44.9 1.0
OD1 B:ASN795 4.2 32.8 1.0
C B:SER794 4.4 35.6 1.0
ND2 B:ASN786 4.4 42.1 1.0
O B:GLY868 4.5 43.9 1.0
CA B:SER794 4.6 31.5 1.0
CG B:ASN786 4.7 51.7 1.0
CG B:ASN795 4.8 34.8 1.0
P E:DG5 4.8 49.4 1.0

Magnesium binding site 6 out of 6 in 5gwi

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Magnesium binding site 6 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:59.0
occ:1.00
 N7 F:DG17 4.6 40.2 1.0
O6 F:DG17 4.6 52.3 1.0
O6 F:DG18 4.8 44.0 1.0
C5 F:DC16 4.9 32.8 1.0

Reference:

Y.R.Wang, S.F.Chen, C.C.Wu, Y.W.Liao, T.S.Lin, K.T.Liu, Y.S.Chen, T.K.Li, T.C.Chien, N.L.Chan. Producing Irreversible Topoisomerase II-Mediated Dna Breaks By Site-Specific Pt(II)-Methionine Coordination Chemistry Nucleic Acids Res. V. 45 10861 2017.
ISSN: ESSN 1362-4962
PubMed: 28977631
DOI: 10.1093/NAR/GKX742
Page generated: Sun Sep 29 15:28:11 2024

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